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SCAN.UPC

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A package Facilitates personalized-medicine workflows, based on a microarray normalization method. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. It can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.

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SCAN.UPC forum

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SCAN.UPC classification

SCAN.UPC specifications

Unique identifier:
OMICS_02006
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
MIT License
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Maintained:
Yes

SCAN.UPC distribution

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SCAN.UPC support

Documentation

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.